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Senftleber NK, Andersen MK, Jørsboe E, Stæger FF, Nøhr AK, Garcia-Erill G, Meisner J, Santander CG, Balboa RF, Gilly A, Bjerregaard P, Larsen CVL, Grarup N, Jørgensen ME, Zeggini E, Moltke I, Hansen T, Albrechtsen A. GWAS of lipids in Greenlanders finds association signals shared with Europeans and reveals an independent PCSK9 association signal. Eur J Hum Genet 2024; 32:215-223. [PMID: 37903942 PMCID: PMC10853193 DOI: 10.1038/s41431-023-01485-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 09/14/2023] [Accepted: 10/11/2023] [Indexed: 11/01/2023] Open
Abstract
Perturbation of lipid homoeostasis is a major risk factor for cardiovascular disease (CVD), the leading cause of death worldwide. We aimed to identify genetic variants affecting lipid levels, and thereby risk of CVD, in Greenlanders. Genome-wide association studies (GWAS) of six blood lipids, triglycerides, LDL-cholesterol, HDL-cholesterol, total cholesterol, as well as apolipoproteins A1 and B, were performed in up to 4473 Greenlanders. For genome-wide significant variants, we also tested for associations with additional traits, including CVD events. We identified 11 genome-wide significant loci associated with lipid traits. Most of these loci were already known in Europeans, however, we found a potential causal variant near PCSK9 (rs12117661), which was independent of the known PCSK9 loss-of-function variant (rs11491147). rs12117661 was associated with lower LDL-cholesterol (βSD(SE) = -0.22 (0.03), p = 6.5 × 10-12) and total cholesterol (-0.17 (0.03), p = 1.1 × 10-8) in the Greenlandic study population. Similar associations were observed in Europeans from the UK Biobank, where the variant was also associated with a lower risk of CVD outcomes. Moreover, rs12117661 was a top eQTL for PCSK9 across tissues in European data from the GTEx portal, and was located in a predicted regulatory element, supporting a possible causal impact on PCSK9 expression. Combined, the 11 GWAS signals explained up to 16.3% of the variance of the lipid traits. This suggests that the genetic architecture of lipid levels in Greenlanders is different from Europeans, with fewer variants explaining the variance.
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Affiliation(s)
- Ninna Karsbæk Senftleber
- Clinical Research, Copenhagen University Hospital-Steno Diabetes Center Copenhagen, Herlev, Denmark
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mette K Andersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emil Jørsboe
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Frederik Filip Stæger
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anne Krogh Nøhr
- Center for Clinical Data Science, Department of Clinical Medicine, Aalborg University and Research, Education, and Innovation, Aalborg University Hospital, Aalborg, Denmark
| | - Genis Garcia-Erill
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Meisner
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cindy G Santander
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Renzo F Balboa
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Peter Bjerregaard
- Centre for Public Health in Greenland, National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Christina Viskum Lytken Larsen
- Centre for Public Health in Greenland, National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Greenland Center for Health Research, Institute for Health and Nature, University of Greenland, Nuuk, Greenland
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marit Eika Jørgensen
- Clinical Research, Copenhagen University Hospital-Steno Diabetes Center Copenhagen, Herlev, Denmark
- Centre for Public Health in Greenland, National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Steno Diabetes Center Greenland, Nuuk, Greenland
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Munich, Germany
| | - Ida Moltke
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Ladekarl M, Nøhr AK, Sønderkær M, Dahl SC, Sunde L, Vestereghem C, Mapendano CK, Haslund CA, Pagh A, Carus A, Lörincz T, Nowicka-Matus K, Poulsen LØ, Laursen RJ, Dybkær K, Poulsen BK, Frøkjær JB, Brügmann AH, Ernst A, Wanders A, Bøgsted M, Pedersen IS. Feasibility and early clinical impact of precision medicine for late-stage cancer patients in a regional public academic hospital. Acta Oncol 2023; 62:261-271. [PMID: 36905645 DOI: 10.1080/0284186x.2023.2185542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
AIM Our goal was to describe a precision medicine program in a regional academic hospital, characterize features of included patients and present early data on clinical impact. MATERIALS AND METHODS We prospectively included 163 eligible patients with late-stage cancer of any diagnosis from June 2020 to May 2022 in the Proseq Cancer trial. Molecular profiling of new or fresh frozen tumor biopsies was done by WES and RNAseq with parallel sequencing of non-tumoral DNA as individual reference. Cases were presented at a National Molecular Tumor Board (NMTB) for discussion of targeted treatment. Subsequently, patients were followed for at least 7 months. RESULTS 80% (N = 131) of patients had a successful analysis done, disclosing at least one pathogenic or likely pathogenic variant in 96%. A strongly or potentially druggable variant was found in 19% and 73% of patients, respectively. A germline variant was identified in 2.5%. Median time from trial inclusion to NMTB decision was one month. One third (N = 44) of patients who underwent molecularly profiling were matched with a targeted treatment, however, only 16% were either treated (N = 16) or are waiting for treatment (N = 5), deteriorating performance status being the primary cause of failure. A history of cancer among 1st degree relatives, and a diagnosis of lung or prostate cancer correlated with greater chance of targeted treatment being available. The response rate of targeted treatments was 40%, the clinical benefit rate 53%, and the median time on treatment was 3.8 months. 23% of patients presented at NMTB were recommended clinical trial participation, not dependent on biomarkers. CONCLUSIONS Precision medicine in end-stage cancer patients is feasible in a regional academic hospital but should continue within the frame of clinical protocols as few patients benefit. Close collaboration with comprehensive cancer centers ensures expert evaluations and equality in access to early clinical trials and modern treatment.
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Affiliation(s)
- Morten Ladekarl
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Anne Krogh Nøhr
- Center for Clinical Data Science, Aalborg University and Aalborg University Hospital, Aalborg, Denmark.,Center for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Mads Sønderkær
- Molecular Diagnostics and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Simon Christian Dahl
- Center for Clinical Data Science, Aalborg University and Aalborg University Hospital, Aalborg, Denmark
| | - Lone Sunde
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Charles Vestereghem
- Center for Clinical Data Science, Aalborg University and Aalborg University Hospital, Aalborg, Denmark
| | - Christophe Kamungu Mapendano
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Charlotte Aaquist Haslund
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Anja Pagh
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Andreas Carus
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Tamás Lörincz
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Kinga Nowicka-Matus
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Laurids Ø Poulsen
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | - Karen Dybkær
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Hematology, Aalborg University Hospital, Aalborg, Denmark
| | - Birgitte Klindt Poulsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Clinical Pharmacology, Aalborg University Hospital, Aalborg, Denmark
| | - Jens Brøndum Frøkjær
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Radiology, Aalborg University Hospital, Aalborg, Denmark
| | - Anja Høegh Brügmann
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Pathology, Aalborg University Hospital, Aalborg, Denmark
| | - Anja Ernst
- Molecular Diagnostics and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Alkwin Wanders
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Pathology, Aalborg University Hospital, Aalborg, Denmark
| | - Martin Bøgsted
- Center for Clinical Data Science, Aalborg University and Aalborg University Hospital, Aalborg, Denmark.,Center for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Inge Søkilde Pedersen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Molecular Diagnostics and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
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Nøhr AK, Eriksson H, Hobart M, Moltke I, Buller R, Albrechtsen A, Lindgreen S. Predictors and trajectories of treatment response to SSRIs in patients suffering from PTSD. Psychiatry Res 2021; 301:113964. [PMID: 33975171 DOI: 10.1016/j.psychres.2021.113964] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/21/2021] [Indexed: 11/25/2022]
Abstract
Paroxetine and sertraline are the only FDA approved drugs for treatment of posttraumatic stress disorder (PTSD). Although both drugs show better outcomes than placebo, not all patients benefit from treatment. We examined predictors and latent classes of SSRI treatment response in patients with PTSD. Symptom severity was measured over a 12-week period in 390 patients suffering from PTSD treated with open-label sertraline or paroxetine and a double-blinded placebo. First, growth curve modeling (GCM) was used to examine population-level predictors of treatment response. Second, growth mixture modeling (GMM) was used to group patients into latent classes based on their treatment response trajectories over time and to investigate predictors of latent class membership. Gender, childhood sexual trauma, and sexual assault as index trauma moderated the population-level treatment response using GCM. GMM identified three classes: fast responders, responders with low pretreatment symptom severity and responders with high pretreatment symptom severity. Class membership was predicted based on time since index trauma, severity of depression, and severity of anxiety. The study shows that higher severity of comorbid disorders does not result in an inferior response to treatment and suggests that patients with longer time since index trauma might particularly benefit from treatment with sertraline or paroxetine.
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Affiliation(s)
- Anne Krogh Nøhr
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark; H. Lundbeck A/S, Valby, Copenhagen, Denmark
| | | | - Mary Hobart
- Otsuka Pharmaceutical Development & Commercialization Inc., 508 Carnegie Center Drive, Princeton, NJ 08540, USA
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | | | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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Nøhr AK, Lindow M, Forsingdal A, Demharter S, Nielsen T, Buller R, Moltke I, Vitezic M, Albrechtsen A. A large-scale genome-wide gene expression analysis in peripheral blood identifies very few differentially expressed genes related to antidepressant treatment and response in patients with major depressive disorder. Neuropsychopharmacology 2021; 46:1324-1332. [PMID: 33833401 PMCID: PMC8134553 DOI: 10.1038/s41386-021-01002-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/20/2021] [Accepted: 03/09/2021] [Indexed: 11/08/2022]
Abstract
A better understanding of the biological factors underlying antidepressant treatment in patients with major depressive disorder (MDD) is needed. We perform gene expression analyses and explore sources of variability in peripheral blood related to antidepressant treatment and treatment response in patients suffering from recurrent MDD at baseline and after 8 weeks of treatment. The study includes 281 patients, which were randomized to 8 weeks of treatment with vortioxetine (N = 184) or placebo (N = 97). To our knowledge, this is the largest dataset including both gene expression in blood and placebo-controlled treatment response measured by a clinical scale in a randomized clinical trial. We identified three novel genes whose RNA expression levels at baseline and week 8 are significantly (FDR < 0.05) associated with treatment response after 8 weeks of treatment. Among these genes were SOCS3 (FDR = 0.0039) and PROK2 (FDR = 0.0028), which have previously both been linked to depression. Downregulation of these genes was associated with poorer treatment response. We did not identify any genes that were differentially expressed between placebo and vortioxetine groups at week 8 or between baseline and week 8 of treatment. Nor did we replicate any genes identified in previous peripheral blood gene expression studies examining treatment response. Analysis of genome-wide expression variability showed that type of treatment and treatment response explains very little of the variance, a median of <0.0001% and 0.05% in gene expression across all genes, respectively. Given the relatively large size of the study, the limited findings suggest that peripheral blood gene expression might not be the best approach to explore the biological factors underlying antidepressant treatment.
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Affiliation(s)
- Anne Krogh Nøhr
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
- H. Lundbeck A/S, Valby, Copenhagen, Denmark.
| | | | | | | | | | | | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | | | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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5
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Nøhr AK, Hanghøj K, Erill GG, Li Z, Moltke I, Albrechtsen A. NGSremix: A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data. G3 (Bethesda) 2021; 11:6279082. [PMID: 34015083 PMCID: PMC8496226 DOI: 10.1093/g3journal/jkab174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/03/2021] [Indexed: 12/04/2022]
Abstract
Estimation of relatedness between pairs of individuals is important in many genetic research areas. When estimating relatedness, it is important to account for admixture if this is present. However, the methods that can account for admixture are all based on genotype data as input, which is a problem for low-depth next-generation sequencing (NGS) data from which genotypes are called with high uncertainty. Here, we present a software tool, NGSremix, for maximum likelihood estimation of relatedness between pairs of admixed individuals from low-depth NGS data, which takes the uncertainty of the genotypes into account via genotype likelihoods. Using both simulated and real NGS data for admixed individuals with an average depth of 4x or below we show that our method works well and clearly outperforms all the commonly used state-of-the-art relatedness estimation methods PLINK, KING, relateAdmix, and ngsRelate that all perform quite poorly. Hence, NGSremix is a useful new tool for estimating relatedness in admixed populations from low-depth NGS data. NGSremix is implemented in C/C++ in a multi-threaded software and is freely available on Github https://github.com/KHanghoj/NGSremix.
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Affiliation(s)
- Anne Krogh Nøhr
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark.,H. Lundbeck A/S, 2500 Valby, Denmark
| | - Kristian Hanghøj
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Genis Garcia Erill
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Zilong Li
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
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Pai S, Weber P, Isserlin R, Kaka H, Hui S, Shah MA, Giudice L, Giugno R, Nøhr AK, Baumbach J, Bader GD. netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks. F1000Res 2020; 9:1239. [PMID: 33628435 PMCID: PMC7883323 DOI: 10.12688/f1000research.26429.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 12/15/2022] Open
Abstract
Patient classification based on clinical and genomic data will further the goal of precision medicine. Interpretability is of particular relevance for models based on genomic data, where sample sizes are relatively small (in the hundreds), increasing overfitting risk netDx is a machine learning method to integrate multi-modal patient data and build a patient classifier. Patient data are converted into networks of patient similarity, which is intuitive to clinicians who also use patient similarity for medical diagnosis. Features passing selection are integrated, and new patients are assigned to the class with the greatest profile similarity. netDx has excellent performance, outperforming most machine-learning methods in binary cancer survival prediction. It handles missing data – a common problem in real-world data – without requiring imputation. netDx also has excellent interpretability, with native support to group genes into pathways for mechanistic insight into predictive features. The netDx Bioconductor package provides multiple workflows for users to build custom patient classifiers. It provides turnkey functions for one-step predictor generation from multi-modal data, including feature selection over multiple train/test data splits. Workflows offer versatility with custom feature design, choice of similarity metric; speed is improved by parallel execution. Built-in functions and examples allow users to compute model performance metrics such as AUROC, AUPR, and accuracy. netDx uses RCy3 to visualize top-scoring pathways and the final integrated patient network in Cytoscape. Advanced users can build more complex predictor designs with functional building blocks used in the default design. Finally, the netDx Bioconductor package provides a novel workflow for pathway-based patient classification from sparse genetic data.
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Affiliation(s)
- Shraddha Pai
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Philipp Weber
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Ruth Isserlin
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Hussam Kaka
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Shirley Hui
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | | | - Luca Giudice
- Department of Computer Science, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Anne Krogh Nøhr
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.,H. Lundbeck A/S, Copenhagen, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.,TUM School of Life Sciences Wiehenstephan, Technical University of Munich, Munich, Germany
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,The Lunenfeld-Tanenbaum Research Institute, Mount Sinal Hospital, Toronto, Canada
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